An eigenvalue analysis obtained from FE software will usually have nothing to do with damping. It involves only the mass and stiffness matrices. A special form of linear system eigenvalue analysis known as "complex mode analysis" does incorporate a damping matrix, but I know of no commercial FE package which does this. In fact FE pacakages are notoriously poor for their representation of damping. The vast majority only allow simple viscous damping models, usually mass proportional damping or mass and stiffness proportional (Rayleigh) damping, to be included in a dynamic model. These damping models often bear little resemblence to any real world damping levels.
"Generalised mass" is a term which usually means a representation of the "physical" mass matrix which has been transformed from "physical" (also called "nodal" in FE) coordinates to generalised (also called "modal"

coordinates.
The eigenvalue analysis produces eigenvalues, which are related to the system natural frequencies (actually 2*pi*f^2), and eigenvectors, which are the mode shapes associated with each of those frequencies. If all these eigenvectors put together into one matrix, with each column of the matrix being one eigenvector, then we have the "modal matrix" of the system. Each column may be scaled in any way you wish. Often the columns are scaled so that each has a maximum value of 1.
The physical mass, stiffness and (if needed) damping matrices can be converted to generalised coordinates by post-multiplying by the modal matrix and pre-multiplying by the transpose of the modal matrix.
These new generalised mass and stiffness matrices will always be diagonal. The same is true of the damping matrix provided a Rayleigh damping model has been assumed. There is now a generalised mass, stiffness and damping value associated with each mode. However, these generalised values are not unique. They depend entirely on the scaling of the eigenvectors in the modal matrix. A generalised mass matrix is pretty useless unless you know the modal matrix which was used to calculate it.
One form of modal scaling which is often used is "unity modal mass". The modal matrix is scaled such that the generalised mass matrix is the identity matrix.
I hope this sheds some light on your problem, but I must stress again that generalised mass values have nothing to do with damping.
Michael